This year we are again participating in the many projects relating to the analysis of peptides and proteins that have been brought to our attention by researchers at NHLBI and NIH. The goal is still to use advanced mass spectrometric technology to study the biology of a particular system by obtaining information on the identity of proteins either through mass spectrometric sequencing or by simply carefully measuring the masses of a sufficient number of its peptides. This technique is unique in identifying post-translational modifications (PTMs) essential for protein/cellular functions. With the state-of-the-art Micromass QTOF3 mass spectrometer and other LC-MS and MALDI-TOF instruments, we were able to perform many experiments on biological samples, mostly in this protein and peptide class. In addition,we seek new chemical methods to enhance the search routines in order to increase their reliability. Currently we are studying the proteomics of lung and Chinese hamster ovary cells, phosphorylation of mitochondrial proteins (Balaban), identifying tumor susceptibility proteins, and determining their modifications. We continue to be involved in the study of compounds with activity in reducing multidrug resistance in chemotherapy and have prepared a radioactive form (J. Ludwig, G. Szakacs, M. Gottesman)and the drug is currently in preclinical trials. We are now preparing many derivatives to identify pertinant features. We continue to spend a significant amount of time optimizing sensitivity and resolution of our QTOF3,its capillary LC and its communication with the mass spectrometer, in particular with regard to its ability to analyze proteins as opposed to peptides.